PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID LOC_Os10g39130.1
Common NameLOC4349237, MADS56, Os10g0536100, OsJ_32282, OSJNBb0060I05.3
Organism
Oryza sativa subsp. japonica
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa
Family MIKC_MADS
Protein Properties Length: 234aa    MW: 26305.1 Da    PI: 10.0264
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os10g39130.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF93.88.1e-30959151
                      S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
            SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                      krien + rqvtfskRrng+lKKA+ELSvLCdaeva+i+fs++g+lye++s
  LOC_Os10g39130.1  9 KRIENPTSRQVTFSKRRNGLLKKAFELSVLCDAEVALIVFSPRGRLYEFAS 59
                      79***********************************************86 PP
2K-box614.6e-2179171698
             K-box   6 gksleeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkl 98 
                       ++++ +++ ++ + +   L k++e L ++ R++lGe+Le  s++eL+ Le +Leksl kiR kK+ell +qi +l++ke+ l ++n++Lr k 
  LOC_Os10g39130.1  79 NNKTIQQDIQQVKDDTLGLAKKLEALDESRRKILGENLEGFSIEELRGLEMKLEKSLHKIRLKKTELLEQQIAKLKEKERTLLKDNENLRGKH 171
                       445678889999*****************************************************************************9885 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004324.1E-39160IPR002100Transcription factor, MADS-box
PROSITE profilePS5006631.314161IPR002100Transcription factor, MADS-box
SuperFamilySSF554552.09E-31385IPR002100Transcription factor, MADS-box
PRINTSPR004041.2E-30323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
CDDcd002652.89E-41379No hitNo description
PfamPF003194.6E-271057IPR002100Transcription factor, MADS-box
PRINTSPR004041.2E-302338IPR002100Transcription factor, MADS-box
PRINTSPR004041.2E-303859IPR002100Transcription factor, MADS-box
PfamPF014868.3E-2184170IPR002487Transcription factor, K-box
PROSITE profilePS5129713.49487177IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010048Biological Processvernalization response
GO:0048510Biological Processregulation of timing of transition from vegetative to reproductive phase
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0046983Molecular Functionprotein dimerization activity
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0020039anatomyleaf lamina
Sequence ? help Back to Top
Protein Sequence    Length: 234 aa     Download sequence    Send to blast
MVRGRTELKR IENPTSRQVT FSKRRNGLLK KAFELSVLCD AEVALIVFSP RGRLYEFASA  60
PSLQKTIDRY KAYTKDHVNN KTIQQDIQQV KDDTLGLAKK LEALDESRRK ILGENLEGFS  120
IEELRGLEMK LEKSLHKIRL KKTELLEQQI AKLKEKERTL LKDNENLRGK HRNLEAAALV  180
ANHMTTTTAP AAWPRDVPMT SSTAGAADAM DVETDLYIGL PGTERSSNRS ETG*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A9e-18177176MEF2C
5f28_B9e-18177176MEF2C
5f28_C9e-18177176MEF2C
5f28_D9e-18177176MEF2C
6byy_A9e-18177176MEF2 CHIMERA
6byy_B9e-18177176MEF2 CHIMERA
6byy_C9e-18177176MEF2 CHIMERA
6byy_D9e-18177176MEF2 CHIMERA
6bz1_A9e-18177176MEF2 CHIMERA
6bz1_B9e-18177176MEF2 CHIMERA
6bz1_C9e-18177176MEF2 CHIMERA
6bz1_D9e-18177176MEF2 CHIMERA
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.378130.0callus| flower| leaf| panicle| root| seed| stem
Expression -- Microarray ? help Back to Top
Source ID
Expression AtlasP0C5B2
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor.
Function -- GeneRIF ? help Back to Top
  1. OsMADS50 and OsMADS56 function antagonistically in regulating long day-dependent flowering by controlling expression of OsLFL1 and Ehd1.
    [PMID: 19558411]
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os10g39130.1
Interaction ? help Back to Top
Source Intact With
BioGRIDLOC_Os10g39130
IntActSearch P0C5B2
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs10g39130
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK0701350.0AK070135.1 Oryza sativa Japonica Group cDNA clone:J023043P08, full insert sequence.
GenBankAY5519190.0AY551919.1 Oryza sativa (japonica cultivar-group) MADS-box protein RMADS214 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015614799.11e-171MADS-box transcription factor 56
SwissprotP0C5B21e-172MAD56_ORYSJ; MADS-box transcription factor 56
TrEMBLA0A0E0R1U41e-169A0A0E0R1U4_ORYRU; Uncharacterized protein
TrEMBLA0A0E0R1U51e-170A0A0E0R1U5_ORYRU; Uncharacterized protein
STRINGORUFI10G17990.11e-170(Oryza rufipogon)
STRINGOS10T0536100-011e-170(Oryza sativa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP14133379
Representative plantOGRP1617761
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G22950.18e-69AGAMOUS-like 19
Publications ? help Back to Top
  1. Cooper B, et al.
    A network of rice genes associated with stress response and seed development.
    Proc. Natl. Acad. Sci. U.S.A., 2003. 100(8): p. 4945-50
    [PMID:12684538]
  2. Rice Chromosome 10 Sequencing Consortium
    In-depth view of structure, activity, and evolution of rice chromosome 10.
    Science, 2003. 300(5625): p. 1566-9
    [PMID:12791992]
  3. Kikuchi S, et al.
    Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.
    Science, 2003. 301(5631): p. 376-9
    [PMID:12869764]
  4. Lee S, et al.
    Systematic reverse genetic screening of T-DNA tagged genes in rice for functional genomic analyses: MADS-box genes as a test case.
    Plant Cell Physiol., 2003. 44(12): p. 1403-11
    [PMID:14701936]
  5. Ryu CH, et al.
    OsMADS50 and OsMADS56 function antagonistically in regulating long day (LD)-dependent flowering in rice.
    Plant Cell Environ., 2009. 32(10): p. 1412-27
    [PMID:19558411]
  6. Bai Z, et al.
    The impact and origin of copy number variations in the Oryza species.
    BMC Genomics, 2016. 17: p. 261
    [PMID:27025496]
  7. Shibaya T, et al.
    Hd18, Encoding Histone Acetylase Related to Arabidopsis FLOWERING LOCUS D, is Involved in the Control of Flowering Time in Rice.
    Plant Cell Physiol., 2016. 57(9): p. 1828-38
    [PMID:27318280]
  8. Han Z,Zhang B,Zhao H,Ayaad M,Xing Y
    Genome-Wide Association Studies Reveal that Diverse Heading Date Genes Respond to Short and Long Day Lengths between Indica and Japonica Rice.
    Front Plant Sci, 2016. 7: p. 1270
    [PMID:27621738]